ShotgunFunctionalizeR

Introduction

ShotgunFunctionalizeR is an R-package for functional comparison of metagenomes. The package contains tools for importing, annotating and visualising metagenomic data produced by shotgun high-throughput sequencing. ShotgunFunctionalizeR contains several statistical procedures for assessing functional differences between samples, both for individual genes and for entire pathways. In addition to standard and previously published methods, we have developed and implemented a novel approach based on a Poisson model. This procedure is highly flexible and thus applicable to a wide range of different experimental designs. Further information about is available in Kristiansson, Hugenholtz and Dalevi 2009 or in a recent poster presented at FEMS 2009 in Gothenburg.

News

2010-10-26 ShotgunFunctionalizeR 1.2-9 is now available where a number of bugs introduced in the latest release have been removed. Minor changes has also been made to the reference manual.
2010-10-20 ShotgunFunctionalizeR 1.2-8 is now availalbe. New features include
  • Support for PFAM, TIGRFAM and custom annotation
  • Several new functions for manipulation of data objects
  • Basic methodology for assessing functional diversity (rarefaction curve analysis, Chao-estimator, clustering)
  • Many bugfixes, some speedups (and probably some new novel bugs as well!)
  • Updated user's guide and reference manual
The new version is available for Unix/Linux, Windows and Mac OS X.
2009-10-12 ShotgunFunctionalizeR 1.0-3 is now available. This release fixes a critical bug where annotations of gene families could, in rare situations, be mixed up. We have also made significant changes for the p-value calculations in the Poisson model, which will now be more robust (we now use chi-squared tests of the residual deviance instead of Wald tests of the regression coefficients).
2009-09-18 ShotgunFunctionalizeR 1.0-2 is now available. This release contains mainly bug fixed.
2009-08-21 A paper describing ShotgunFunctionalizeR has now been published in Bioinformatics.
2009-08-17 We have now added support for Mac OS X.
2009-07-07 ShotgunFunctionalizeR 1.0-1 has now been released. This version contains a few bug fixes as well as the missing manual pages. The reference manual has also be updated.
2009-07-03 ShotgunFunctionalizeR 1.0 has now been released. This version is the first final version (which doesn't mean that it is bug free). Changes includes mostly bug fixes. The User's Guide and Reference Manual has also been updated.
2009-06-27 Two example datasets (Ocean's Interior and Mouse Gut) is now available as download in ShotgunFunctionalizeR compatible format.
2009-06-23 ShotgunFunctionalizeR 0.0-13 is now available.
2009-05-12 ShotgunFunctionalizeR 0.0-12 is available for download. New functions include the groupPlot function (to plot results after direct comparions between groups using the Poisson model). The User Guide has been updated with examples.

Downloads

The R-package
Older versions of ShotgunFunctionalizeR can be found here.

Documentation
Example metagenomes

Requirements and Installation

ShotgunFunctionalizeR is dependent on the multtest package (Pollard at al., 2004), which is a part of the Bioconductor software project. This means that the Bioconductor needs to be installed on your computer before ShotgunFunctionalizeR can function properly. To install Bioconductor, start R and type: 
> source("http://bioconductor.org/biocLite.R")
> biocLite()
After the installation of Bioconductor have finished, you can install ShotgunFunctionalizeR by typing: 
> install.packages("ShotgunFunctionalizeR", contriburl="http://shotgun.zool.gu.se")

Citing ShotgunFunctionalizeR

If you use ShotgunFunctionalizeR in your research, please cite:

Kristiansson E, Hugenholtz P and Dalevi D. (2009). ShotgunFunctionalizeR: An R-package for functional comparisons of metagenomes. Bioinformatics. doi:10.1093/bioinformatics/btp508.

Contacts

Contact Erik Kristiansson (erik.kristiansson@neuro.gu.se) or Daniel Dalevi (daniel.dalevi@gmail.com) for more information.
Version 1.0 (last updated: 2010-10-26) Rlogo